I am trying to use “Relax pdb with allatom constraints” to prepare starting files. This works fine as long as the input pdb contains only a single chain. If it contains two chains, relaxation fails (see attached log file). Although each of the component chains runs fine on its own, as soon as I try to process the complex, the process fails with a complaint about missing atoms:
“[ERROR] Exception caught by JobDistributor for job Graft_FV_0001_0001Atom CG 122 not found”
While sidechain_cst_3.py attempts to match the internal Rosetta numbering scheme when generating constraints, it doesn’t always get things right. By doing the constraint generation within Rosetta itself, it’s easier to get right.